The absorbance and fluorescence characteristics of colored dissolved organic matter (CDOM) were investigated in the tropical monsoonal Godavari estuary over a year during 18 field surveys attempting to capture different river discharge scenarios ranging from nil to >5000 ms ⁻¹ and the accompanying environmental factors. Key biogeochemical constituents were also analyzed to explain the abundance and structure of CDOM and fluorescent DOM (FDOM) in terms of spatiotemporal controls. The high flow water of the monsoon season was rich in CDOM of spectral slope (${\mathit{S}}_{300-500}$) typical for river water but of lower fluorescence. The first flood water was most rich in CDOM of lowest ${\mathit{S}}_{300-500}$, attributed to land washings during summer. The ratio between the UV–visible​ humic-like (A) and marine humic-like (M) fluorophores was linearly related to that of tryptophan protein-like (T) and Tyrosine protein-like (B) fluorophores and indicated linkage between terrestrial inputs and marine processes. The low and nil flow water was composed of seasonally and spatially variable CDOM but which was conservative against salinity (S) fitting to the model, a${}_{\mathrm{CDOM}}$(350) (m⁻¹) = 2.196-0.036*S. During the discharge season, pH held an inverse linear relationship to $a_{\mathrm{CDOM}}$(350): a₃₅₀ (m⁻¹) = 9.346-0.535*pH. The salinity co-varying (conservative) CDOM was linear versus silicate. A laboratory experiment showed that CDOM, FDOM and silicate were co-leached from the estuarine silts. During the non-discharge season unique, transient factors affected the CDOM e.g., (i) hot summer conditions in the upper estuary, (ii) benthic flux by bacterial metabolism from the consolidated silts after the flood season, and (iii) occasional anthropogenic input of petroleum hydrocarbons. The B:T fluorophore ratio was higher and linear versus NH${}_4^{+}$ during no-discharge and is a potential index of the bacterial metabolism i.e., protein un-folding of the silt-held organic matter accumulated during the erstwhile flood season.