Benthic diatoms are important components of marine shallow-water habitats that may affect primary production, stabilize sediment, and produce extracellular polymeric substances. Benthic diatoms are useful for estimating the trophic status of marine ecosystems. In this study, we investigated the diversity and abundance of benthic diatoms to integrate these data with the physicochemical characteristics of shallow coastal areas in Negeri Sembilan. A total of 39 species of epipelic diatoms were extracted by removing organic matter from sediments that were dominated by pennate diatoms. Results showed that Diploneis crabro, Eunotogramma laevis, Actinoptychus sp., and Cocconeisplacentula were the important species in the area. The abundance varied between 1.85 × 103 and 3.43 × 103 cells/g, and the diversity index fluctuated between 2.13 and 2.58. The abundance had significant positive correlations with seawater surface temperature (SST) but had negative correlations with pH and NH3. The diversity on the other end was positively correlated with SST but negatively correlated with total suspended solids and SiO2. Principal component analysis (PCA) demonstrated that the abundance of D. crabro, E. laevis, and Actinoptychus sp. can be attributed to high levels of NO2−, NH3, and total dissolved solids. PCA also showed positive correlations of C. placentula with NO3−and SiO2 but negative ones with PO43− and pH. The epipelic diatom community showed high diversity with high variations throughout the study area.