Coastal waters are currently receiving anthropogenic impacts from the mainland that caused the natural conditions to change to higher nutrient content. This study was conducted to examine the spatial and temporal dynamics of trophic status and how zone location and rainfall category affect the distribution of trophic status. Water quality data were collected for 6 months with different rainfall intensities at 16 observation stations. Trophic status was determined using the TRIX index which combines biological, physical, and chemical water variables. Rainfall had no significant effect on the TRIX index with a p-value of 0.223 (>0.05), but the distance from the land had a significant effect with a p-value of (<2e-16). In coastal waters in the 1st zone, the average TRIX value was 5.93 ± 0.23 (high trophic status/eutrophy that tends to be very high/hypertrophy), in the 2nd zone was 5.49 ± 0.21 (high trophic status/moderate trophy), in the 3rd zone was 5.23 ± 0.25 (high trophic status/eutrophy that is slightly low) and in the 4th zone was 4.47 ± 0.47 (moderate trophic status/mesotrophy). Based on PCA analysis and correlation for water quality data, Index TRIX had a strong positive correlation with phosphate (0.92), TSS (0.91), chlorophyll-a (0.089), temperature (0.88), nitrate (0.83), and moderate positive correlation with turbidity (0.68). In addition, the TRIX index had a strong negative correlation with salinity (-0.85), a moderate negative correlation with TDS (-0.77) and DO (-0.62), and a weak correlation with pH (-0.09). There has been eutrophication in coastal areas, especially in the near shoreline zone and tends to decrease at more distant locations. It is necessary to manage anthropogenic waste based on quality standards to ensure that coastal waters are healthy and support sustainable ecosystems