This study aimed to describe the correlation between water quality, phytoplankton abundance, and diversity in Balikpapan Bay, where the Indonesian government plans to move the national capital city. Observations were made at eight stations to collect data on water quality and phytoplankton during the neap tide. Phytoplankton were found in nine species during floods and thirteen during ebb tides. The most dominant species was Cyclotella sp., with the most prevalent class being Bacillariophyceae (diatoms). Phytoplankton diversity is considered a low category with an index of diversity (H′) average of 1.08±0.35 (1.02±0.53) during flood (ebb) tides, and generally, there are no dominant species. The Bray-Curtis dissimilarity index showed that species similarities were approximately 96.50% (93.25%) during flood (ebb) tides. Principal component analysis (PCA) results showed that the downstream area was influenced by salinity and current speed, whereas the upstream region was influenced by chlorophyll-a, temperature, nitrate, and turbidity. This situation also shows that phytoplankton diversity (H′) is affected more by salinity, turbidity, current speed, and chlorophyll-a. At the same time, the index of dominance (C) was influenced by temperature, current speed, and chlorophyll-a content. Thus, dynamic conditions should be considered as factors influencing the phytoplankton abundance and dynamics in Balikpapan Bay.