Small-scale fisheries are significant sources of nutrition and livelihood globally. However, increasing anthropogenic activities in coastal areas of developing countries have threatened the sustainability of artisanal fisheries and species. Fisheries of Sardinella maderensis, towards the global stock of which Nigeria contributes 9% and which is a significant livelihood source in the coastal communities of Ibeju-Lekki, Lagos, faces sustainability threats. This research investigated the effects of anthropogenic activities on S. maderensis fisheries in the coastal areas of Ibeju-Lekki, Lagos, Nigeria. The study adopted a mixed-method approach involving qualitative and quantitative research methods. These included species identification, water quality analysis, land-use change analysis, field surveys, focus group discussions, and interviews. Genetic analysis of the fish samples from the study area revealed that the species had a mean of 98% similarity to S. maderensis. While major urban and industrial land use has increased by 175% in the last four decades, the catch per unit effort (CPUE) of S. maderensis declined monthly to 0.0072 kg/H between 2003 and 2019. Linear regression indicated that anthropogenic variables explained approximately 39.58% of the variation in the CPUE (p < 0.001, R2 = 0.40). Water samples showed that heavy metal levels were above international limits, with high total petroleum hydrocarbon (TPH) pollution in all stations (27.56 mg/L–3985.40 mg/L). Physiochemical analysis of water samples indicated TDS levels higher than the acceptable limits (mean = 24,971.1 mg/L) and inadequate chlorophyll-a levels (mean = 0.01 µg/L). Hence, urgent strategies are required to mitigate anthropogenic threats through inclusive coastal management policies supporting resilient artisanal fisheries.