Marine environmental pollution from urban development, tourism industry and agricultural activities affects the quality of marine and aquatic life and humans. This study established the impact of anthropogenic activities on marine water nutrient loading and primary productivity at Mtwapa Creek in Kenya. Triplicate water samples were collected twice a month from seven (7) sites on the creek to determine the levels of concentration of the three nutrients; PO − 4 , NO − 3 and NH 3 in creek waters. Samples were analyzed for nutrients level using the spectrophotometric method. Primary productivity as an indication of carbon assimilation was computed using the traditional Winkler method. Quantitative one-way Analysis of Variance was used to determine the variations between sampling sites while correlation analysis was computed to establish the relationship between nutrients and carbon levels. There was spatial and temporal fluctuation of nutrients levels on the creek; however the levels of nitrates were within the oligotrophic range. Phosphate levels were not significantly different throughout the sampling period, while Ammonia levels were very significantly high in the creek waters, implying active biochemical processes affecting primary productivity with phosphates greatly influencing carbon assimilation. Strategic land based management approaches should be instituted to reduce the discharge flow into the creek waters.