Phytoplankton growth is influenced by the presence of nutrients N and P. Each region has a specific N/P ratio, due to the influence of anthropogenic inputs. This study aimed to assess the response of phytoplankton chlorophyll-a biomass due to differences in N/P ratio by the influence of river flow in the north coast of Java; Jobokuto Bay (Jepara), The coastal waters of Semarang and the front of the Cisadane river. N-nutrients were analyzed in the form of N-NO3 (nitrate) and N-NH4+ (ammonium ions), and orthophosphate ions (P-PO42-). Nutrient analysis was spectrometric, using the reduction methods (nitrate), ammonium (indophenol-blue), and phosphate (molybdenum-blue). Test for site differences using Kruskall-Wallis, followed by a posthoc test. The results showed that Semarang waters had a lower N/P (Stoichiometric) ratio than Jepara and Cisadane, which can be used to predict that P nutrient input is higher than N. This high P input impacts microalgal development (chlorophyll-a). In addition, we also found Semarang waters to have higher speciation of inorganic N in the form of ammonium, which is one of the drivers of eutrophication in these waters. The use of a ratio of N/P is very important in estimating the eutrophication process and can be used to estimate the dominance of nutrients entering the water due to anthropogenic activities in the upstream area.