Detecting Network Anomalies with Zeek

When to Use

• Deploying passive network security monitoring at key network choke points for continuous visibility
• Generating structured connection, DNS, HTTP, SSL, and file transfer logs for SIEM ingestion and threat hunting
• Writing custom Zeek scripts to detect organization-specific threats, policy violations, or beaconing behavior
• Performing retrospective analysis on network metadata to investigate security incidents
• Complementing IDS solutions with protocol-level metadata analysis that signature-based tools may miss

Do not use as a replacement for inline IDS/IPS that can actively block traffic, for monitoring encrypted payloads without TLS inspection, or on endpoints where host-based agents are more appropriate.

Prerequisites

• Zeek 6.0+ installed from source or package manager (

  zeek --version

  )
• Network interface configured on a span port, network tap, or virtual switch mirror for passive capture
• Sufficient disk storage for log files (estimate 1-5 GB/day per 100 Mbps of monitored traffic)
• Familiarity with Zeek's scripting language for writing custom detections
• Log aggregation system (Splunk, Elastic, Graylog) for centralized analysis

Workflow

Step 1: Install and Configure Zeek

# Install Zeek on Ubuntu/Debian
sudo apt install -y zeek

# Or install from source for latest version
git clone --recursive https://github.com/zeek/zeek
cd zeek && ./configure --prefix=/opt/zeek && make -j$(nproc) && sudo make install
export PATH=/opt/zeek/bin:$PATH

# Configure the monitoring interface
sudo vi /opt/zeek/etc/node.cfg

# /opt/zeek/etc/node.cfg
[zeek]
type=standalone
host=localhost
interface=eth1

# Configure local network definitions
sudo vi /opt/zeek/etc/networks.cfg

# /opt/zeek/etc/networks.cfg
10.0.0.0/8       Internal
172.16.0.0/12    Internal
192.168.0.0/16   Internal

# Disable NIC offloading for accurate packet capture
sudo ethtool -K eth1 rx off tx off gro off lro off tso off gso off

# Deploy Zeek
sudo zeekctl deploy

# Verify Zeek is running
sudo zeekctl status

Step 2: Understand and Navigate Zeek Logs

# Zeek generates structured log files in /opt/zeek/logs/current/
ls /opt/zeek/logs/current/

# Key log files:
# conn.log       - All network connections (TCP, UDP, ICMP)
# dns.log        - DNS queries and responses
# http.log       - HTTP requests and responses
# ssl.log        - SSL/TLS handshake details
# files.log      - File transfers observed on the network
# notice.log     - Alerts from Zeek detection scripts
# weird.log      - Protocol anomalies and errors
# x509.log       - X.509 certificate details
# smtp.log       - SMTP email transactions
# ssh.log        - SSH connection details

# View connection log with zeek-cut for column selection
cat /opt/zeek/logs/current/conn.log | zeek-cut ts id.orig_h id.orig_p id.resp_h id.resp_p proto service duration orig_bytes resp_bytes

# View DNS log
cat /opt/zeek/logs/current/dns.log | zeek-cut ts id.orig_h query qtype_name answers

# View HTTP log
cat /opt/zeek/logs/current/http.log | zeek-cut ts id.orig_h host uri method status_code user_agent

Step 3: Write Custom Detection Scripts

# Create a custom detection script directory
sudo mkdir -p /opt/zeek/share/zeek/site/custom-detections

Create a script for detecting DNS tunneling:

# /opt/zeek/share/zeek/site/custom-detections/dns-tunneling.zeek
@load base/frameworks/notice

module DNSTunneling;

export {
    redef enum Notice::Type += {
        DNS_Tunneling_Detected,
        DNS_Long_Query
    };

    # Threshold: number of unique queries per source in time window
    const query_threshold: count = 200 &redef;
    const time_window: interval = 5min &redef;
    const max_query_length: count = 50 &redef;
}

# Track query counts per source IP
global dns_query_counts: table[addr] of count &create_expire=5min &default=0;

event dns_request(c: connection, msg: dns_msg, query: string, qtype: count, qclass: count)
{
    local src = c$id$orig_h;

    # Check for unusually long domain queries (base64-encoded data)
    if ( |query| > max_query_length )
    {
        NOTICE([
            $note=DNS_Long_Query,
            $msg=fmt("Unusually long DNS query from %s: %s (%d chars)", src, query, |query|),
            $src=src,
            $identifier=cat(src, query)
        ]);
    }

    # Track query volume per source
    dns_query_counts[src] += 1;

    if ( dns_query_counts[src] == query_threshold )
    {
        NOTICE([
            $note=DNS_Tunneling_Detected,
            $msg=fmt("Possible DNS tunneling: %s sent %d queries in %s", src, query_threshold, time_window),
            $src=src,
            $identifier=cat(src)
        ]);
    }
}

Create a script for detecting beaconing:

# /opt/zeek/share/zeek/site/custom-detections/beacon-detection.zeek
@load base/frameworks/notice
@load base/frameworks/sumstats

module BeaconDetection;

export {
    redef enum Notice::Type += {
        Possible_Beaconing
    };

    const beacon_threshold: count = 50 &redef;
    const observation_window: interval = 1hr &redef;
}

event zeek_init()
{
    local r1 = SumStats::Reducer(
        $stream="beacon.connections",
        $apply=set(SumStats::SUM)
    );

    SumStats::create([
        $name="detect-beaconing",
        $epoch=observation_window,
        $reducers=set(r1),
        $threshold_val(key: SumStats::Key, result: SumStats::Result) = {
            return result["beacon.connections"]$sum;
        },
        $threshold=beacon_threshold + 0.0,
        $threshold_crossed(key: SumStats::Key, result: SumStats::Result) = {
            NOTICE([
                $note=Possible_Beaconing,
                $msg=fmt("Possible beaconing: %s made %d connections in %s",
                         key$str, result["beacon.connections"]$sum, observation_window),
                $identifier=key$str
            ]);
        }
    ]);
}

event connection_state_remove(c: connection)
{
    if ( c$id$resp_h !in Site::local_nets )
    {
        local key = fmt("%s->%s:%d", c$id$orig_h, c$id$resp_h, c$id$resp_p);
        SumStats::observe("beacon.connections", [$str=key], [$num=1]);
    }
}

Step 4: Load Custom Scripts and Deploy

# Add custom scripts to local.zeek
sudo tee -a /opt/zeek/share/zeek/site/local.zeek << 'EOF'

# Custom detection scripts
@load custom-detections/dns-tunneling.zeek
@load custom-detections/beacon-detection.zeek

# Enable additional protocol analyzers
@load protocols/ftp/software
@load protocols/http/software
@load protocols/smtp/software
@load protocols/ssh/detect-bruteforcing
@load protocols/ssl/validate-certs
@load protocols/ssl/log-hostcerts-only
@load protocols/dns/detect-external-names

# Enable file extraction
@load frameworks/files/extract-all-files

# Enable Intel framework for threat intelligence
@load frameworks/intel/seen
@load frameworks/intel/do_notice
EOF

# Reload Zeek configuration
sudo zeekctl deploy

# Verify scripts loaded without errors
sudo zeekctl diag

Step 5: Threat Hunting Queries on Zeek Logs

# Find long-duration connections (possible C2)
cat /opt/zeek/logs/current/conn.log | zeek-cut ts id.orig_h id.resp_h id.resp_p duration | \
  awk '$5 > 3600 {print $0}' | sort -t$'\t' -k5 -rn | head -20

# Find connections with high data transfer volumes
cat /opt/zeek/logs/current/conn.log | zeek-cut ts id.orig_h id.resp_h orig_bytes resp_bytes | \
  awk '$4 > 100000000 || $5 > 100000000 {print $0}'

# Identify rare user agents (potential malware)
cat /opt/zeek/logs/current/http.log | zeek-cut user_agent | sort | uniq -c | sort -n | head -20

# Find self-signed or expired certificates
cat /opt/zeek/logs/current/ssl.log | zeek-cut ts id.orig_h id.resp_h server_name validation_status | \
  grep -v "ok"

# Detect DNS queries to newly registered domains (DGA patterns)
cat /opt/zeek/logs/current/dns.log | zeek-cut ts id.orig_h query | \
  awk -F'\t' '{n=split($3,a,"."); if(length(a[n-1]) > 10) print $0}'

# Find SSH brute force attempts
cat /opt/zeek/logs/current/ssh.log | zeek-cut ts id.orig_h id.resp_h auth_success | \
  grep "F" | awk '{print $2}' | sort | uniq -c | sort -rn | head -10

# Identify unusual port usage
cat /opt/zeek/logs/current/conn.log | zeek-cut id.resp_p proto service | \
  sort | uniq -c | sort -rn | head -50

Step 6: Integrate with SIEM and Set Up Alerting

# Configure JSON log output for SIEM ingestion
sudo tee /opt/zeek/share/zeek/site/json-logs.zeek << 'EOF'
@load policy/tuning/json-logs.zeek
redef LogAscii::use_json = T;
EOF

# Forward logs to Elastic via Filebeat
# /etc/filebeat/filebeat.yml
sudo tee /etc/filebeat/filebeat.yml << 'EOF'
filebeat.inputs:
  - type: log
    enabled: true
    paths:
      - /opt/zeek/logs/current/*.log
    json.keys_under_root: true
    json.add_error_key: true
    fields:
      source: zeek
    fields_under_root: true

output.elasticsearch:
  hosts: ["https://elastic-siem:9200"]
  index: "zeek-%{+yyyy.MM.dd}"
  username: "elastic"
  password: "${ES_PASSWORD}"
EOF

sudo systemctl enable --now filebeat

# Set up log rotation
sudo tee /etc/cron.d/zeek-logrotate << 'EOF'
0 0 * * * root /opt/zeek/bin/zeekctl cron
EOF

# Monitor Zeek health
sudo zeekctl status
sudo zeekctl netstats

Key Concepts

Term	Definition
Network Security Monitor	Passive analysis tool that observes network traffic and generates structured metadata logs without altering or blocking traffic flow
Zeek Script	Event-driven scripts written in Zeek's domain-specific language that process network events and generate notices, logs, and metrics
Connection Log (conn.log)	Core Zeek log recording every observed connection with source/destination IPs, ports, protocol, duration, and byte counts
Notice Framework	Zeek subsystem for generating alerts when detection scripts identify suspicious activity, outputting to notice.log
SumStats Framework	Statistical analysis framework in Zeek for tracking metrics over time windows, enabling threshold-based detection of anomalies
Intel Framework	Zeek module for matching observed network indicators against threat intelligence feeds and generating alerts on matches

Tools & Systems

• Zeek 6.0+: Open-source network security monitor generating comprehensive protocol-level logs from passive traffic analysis
• zeek-cut: Zeek utility for extracting specific columns from tab-separated Zeek log files for quick analysis
• zeekctl: Zeek management tool for deploying, monitoring, and managing Zeek instances across single or clustered deployments
• RITA (Real Intelligence Threat Analytics): Open-source tool that analyzes Zeek logs for beaconing, DNS tunneling, and other threat indicators
• Filebeat: Elastic agent for shipping Zeek JSON logs to Elasticsearch for centralized analysis and visualization

Common Scenarios

Scenario: Detecting Command-and-Control Beaconing in Enterprise Traffic

Context: A threat intelligence report indicates that a specific threat actor uses HTTPS beaconing with 60-second intervals to compromised hosts. The SOC team needs to analyze Zeek logs to identify any hosts exhibiting this pattern across the enterprise network carrying 2 Gbps of traffic.

Approach:

1. Deploy Zeek on a network tap at the internet egress point with AF_PACKET for high-throughput capture
2. Enable the custom beacon detection script with thresholds tuned for 60-second intervals over 1-hour observation windows
3. Query conn.log for connections to external IPs with consistent duration and inter-connection timing: filter connections where the standard deviation of inter-arrival times is less than 5 seconds
4. Cross-reference suspicious destination IPs against threat intelligence feeds loaded into Zeek's Intel framework
5. Examine ssl.log for the associated TLS certificates -- check for self-signed certificates, unusual issuer names, or certificates with short validity periods
6. Generate a notice for each identified beaconing source and feed into the SIEM for SOC triage

Pitfalls:

• Not tuning beacon detection thresholds for the environment, resulting in false positives from legitimate update services (Windows Update, AV updates)
• Failing to exclude CDN and cloud service provider IP ranges that naturally receive many repeat connections
• Running Zeek without sufficient CPU cores, causing packet drops on high-throughput links
• Not enabling JSON log output, making SIEM integration unnecessarily complex with custom parsers

Output Format

## Zeek Network Anomaly Detection Report

**Sensor**: zeek-sensor-01 (10.10.1.250)
**Monitoring Interface**: eth1 (span port from Core-SW1)
**Analysis Period**: 2024-03-15 00:00 to 2024-03-16 00:00 UTC
**Total Connections Logged**: 2,847,392

### Anomalies Detected

| Notice Type | Source | Destination | Details |
|-------------|--------|-------------|---------|
| DNS_Tunneling_Detected | 10.10.3.45 | 8.8.8.8 | 847 queries to suspect-domain.xyz in 5 min |
| Possible_Beaconing | 10.10.5.12 | 203.0.113.50:443 | 62 connections with 59.8s avg interval |
| SSL::Invalid_Server_Cert | 10.10.8.22 | 198.51.100.33:443 | Self-signed cert, CN=localhost |
| SSH::Password_Guessing | 45.33.32.156 | 10.10.20.11:22 | 487 failed attempts in 30 min |

### Recommendations
1. Isolate 10.10.3.45 and investigate for DNS tunneling malware
2. Block 203.0.113.50 at firewall and forensically image 10.10.5.12
3. Investigate self-signed TLS certificate on 198.51.100.33
4. Block 45.33.32.156 and enforce SSH key-only authentication