This study assessed background ionizing radiation (BIR) and associated cancer risk across Warri, Koko, and Burutu sea ports in Niger Delta of Nigeria. Thirty-two stratified sampling points were surveyed in situ using a Digilert 100 meter, and results were analyzed with descriptive statistics, Shapiro–Wilktests, one-way ANOVA, and Tukey HSD. Threshold compliance was evaluated against UNSCEAR reference levels (BIR = 0.057 µSv/h; ELCR = 0.29 × 1 0⁻³), while spatial distribution was visualized using thematic risk mapping. To capture uncertainty, Monte Carlo simulations (10,000 iterations per port) modeled ELCR from observed BIR ranges. BIR values varied from 0.008 to 0.014 µSv/h, with Burutu recording the highest mean (0.012 ± 0.002 µSv/h). ANOVA confirmed significant inter-port variation (p = 0.0136), with Burutu significantly higher than both Warri and Koko. Although Burutu showed the lowest BIR exceedance (14.3%), it recorded the highest ELCR exceedance (28.6%), reflecting cumulative radiological risk. Simulated ELCR values were stable across ports (≈ 0.075), with overlapping confidence intervals. Spatial mapping identified elevated clusters in Burutu’s anchoring and storage zones. Compared with Onne Port (mean ELCR = 0.289), the studied seaports presented lower but still concerning risk levels. These findings highlight the need for targeted monitoring, sediment analysis, and geostatistical modeling to strengthen environmental health safeguards in Nigerian coastal ports.