Seasonal and inter-annual variability of hydrological parameters and its impact on chlorophyll distribution was studied from January 2009 to December 2011 at four coastal stations along the southwest Bay of Bengal. Statistical analysis(principal component analysis(PCA), two-way analysis of variance(ANOVA) and correlation analysis)showed the significant impact of hydrological parameters on chlorophyll distribution in the study area. The ranges of different parameters recorded were 23.8–33.8°C(SST), 4.00–36.00(salinity), 7.0–9.2(p H), 4.41–8.32 mg/L(dissolved oxygen), 0.04–2.45 μmol/L(nitrite), 0.33–16.10 μmol/L(nitrate), 0.02–2.51 μmol/L(ammonia),0.04–3.32 μmol/L(inorganic phosphate), 10.09–85.28 μmol/L(reactive silicate) and 0.04–13.8 μg/L(chlorophyll).PCA analysis carried out for different seasons found variations in the relationship between physico-chemical parameters and chlorophyll in which nitrate and chlorophyll were positively loaded at PC1(principal component1) during spring inter-monsoon and at PC2(principal component 2) during other seasons. Likewise correlation analysis also showed significant positive relationship between chlorophyll and nutrients especially with nitrate(r=0.734). Distribution of hydrobiological parameters between stations and distances was significantly varying as evidenced from the ANOVA results. The study found that the spatial and temporal distribution of chlorophyll was highly dependent on the availability of nutrients especially, nitrate in the southwest Bay of Bengal coastal waters. Seasonal and inter-annual variability of hydrological parameters and its impact on chlorophyll distribution was studied from January 2009 to December 2011 at four coastal stations along the southwest Bay of Bengal. Statistical analysis (principal component analysis (PCA), two-way analysis of variance (ANOVA) and correlation analysis) showed the significant impact of hydrological parameters on chlorophyll distribution in the study area. The ranges of different parameters recorded were 23.8-33.8 ° C (SST), 4.00-36.00 (salinity), 7.0-9.2 (p H, 4.41-8.32 mg / L dissolved oxygen, 0.04-2.45 μmol / L nitrite, 0.33-16.10 μmol / L nitrate, 0.02-2.51 μmol / L ammonia, 0.04-3.32 μmol / L ammonia, inorganic phosphate, 10.09-85.28 μmol / L (reactive silicate) and 0.04-13.8 μg / L (chlorophyll) .PCA analysis carried out for different seasons found variations in the relationship between physico-chemical parameters and chlorophyll in which nitrate and chlorophyll were positively loaded at PC1 (principal c Likewise, the correlation between chlorophyll and nutrients with nitrate (r = 0.734) Distribution of hydrobiological parameters between stations and distances was significantly varying as evidenced from the ANOVA results. The study found that the spatial and temporal distribution of chlorophyll was highly dependent on the availability of nutrients especially, nitrate in the southwest Bay of Bengal coastal waters.