Due to rapid urban development in the coastal area of the East Aceh Regency, water quality degradation and marine pollution issues become the primary concern in this region. Moreover, seasonal observation of water quality and phytoplankton has yet to be assessed. This study aimed to determine the control of seasonal water quality and nutrients over phytoplankton abundance throughout the East Aceh coast. Direct field measurements and laboratory analyses were performed to collect the primary data, whereby the sampling period was conducted during the displacement toward the ebb tide. We assessed the water quality parameters using a modified CWQI (coastal water quality index). Furthermore, linear regression and principal component analysis were performed as the basis of statistical analyses. The phytoplankton abundance was higher in April than in September, with most Bacillariophyceae and Dinophyceae in all observed stations. Except for DO and turbidity, the assessed water quality parameters (temperature, TDS, conductivity, salinity, sulfide, and TOM) are feasible for marine biota. Of particular concern, the East Aceh coast is characterized by poor-good water quality, with the CWQI value ranging from 40 to 90. Based on the regression and PCA analyses, N and P nutrients significantly control the phytoplankton abundance like a “seesaw” between April and September, with a respective coefficient determination of about 50%. Because of the tremendously high phosphate observed in April, the water condition tended to be P-limited and vice versa for September. On the other hand, instead of evoking the phytoplankton growth, each water quality parameter has a specific influence in characterizing phytoplankton communities in the study area.