Pigment-producing bacteria are valuable bioresources for industrial applications. This study investigated the isolation of pigment-producing bacteria from three locations of the Netravathi River estuary (NRE-1, NRE-2, and NRE-3) in Mangaluru. Estuarine soil and water samples were collected concurrently with the measurements of physicochemical parameters, including temperature, pH, and salinity. The total viable count and total heterotrophic bacteria (THB) were analyzed. THB populations were differentiated into non-pigmented heterotrophic bacteria (NPHB) and pigmented heterotrophic bacteria (PHB). The PHB/NPHB % recorded was 8.08%, 38.42%, and 20.26% of the isolates at NRE-1, NRE-2, and NRE-3, respectively. With colony-forming units showing minimal variation across different growth media, the PHB recorded was 37.03% of total bacterial isolates. Phylogenetic classification of the pigmented bacteria from the NRE revealed four classes: Alphaproteobacteria (35%), Actinobacteria (30%), Gammaproteobacteria (30%), and Chitinophagia (5%). Based on the Gompertz growth curve model, three strains, Erythrobacter sp. RANMB8, Qipengyuania sp. RANM35, and Zooshikella sp. RANM57, were selected from NRE-1, NRE-2, and NRE-3. The UV absorption spectrum of Zooshikella sp. RANM57, Erythrobacter sp. RANMB8, and Qipengyuania sp. RANM35 exhibited peaks between 430 and 490 nm. Fourier-transform infrared spectroscopy (FTIR) spectrum analysis of Qipengyuania sp. RANM 35 and Erythrobacter sp. B8 exhibited an observed value of 3423.97 with a structure closely related to the standard β-carotene, while Zooshikella sp. RANM57 exhibited a peak at 3339.41, which closely resembled that of the standard for prodigiosin. The isolated pigmented bacteria exhibited seven distinct colors: brown (28%), yellow (21%), red (16%), pink (16%), orange (15%), black (2%), and blue (2%). Gram staining revealed that 45% of the colonies were Gram-negative, 31% Gram-positive, and 16% Gram-positive rods in chains. The remaining 8% displayed varied characteristics, with 16% Gram-positive bacteria belonging to the Actinobacterial family, owing to their slow growth rate. Isolation of pigmented bacteria from NRE poses several challenges. This study revealed that the selected isolates have the potential to produce pigments that can be exploited for bioprospecting in the pigment industry.