Chlorophyll a (Chl-a) has been the most commonly used biomass metric in biological oceanographic processes. Although limited to two-dimensional surfaces, remote-sensing tools have been successfully providing the most recent state of marine phytoplankton biomass to better understand bottom-up processes initiating daily marine material cycles. In this exercise, ocean color products with various time-scales, derived from Sea-Viewing Wide Field-of-View Sensor (SeaWiFS), were used to investigate how their bio-optical properties affect the upper-ocean thermal structure in a global ocean modeling framework. This study used a ¼-degree Hybrid Coordinate Ocean Model forced by hourly atmospheric fluxes from the Climate Forecast System Reanalysis at National Oceanic Atmospheric Administration. Three numerical experiments were prepared by combining two ocean color products – downwelling diffuse attenuation coefficients (K_dPAR) and chlorophyll a (Chl-a) – and two shortwave radiant flux algorithms. These three runs are: (1) KparCLM, based on a 13-year long-term climatological K_dPAR derived from SeaWiFS; (2) ChlaCLM, based on a 13-year long-term Chl-a derived from SeaWiFS; and (3) ChlaID, which uses the inter-annual time-series of monthly-mean SeaWiFS Chl-a product. The KparCLM experiment uses a Jerlov-like two-band scheme; whereas, both ChlaCLM and ChlaID use a two-band scheme that considers inherent (absorption (a) and backscattering (b_b) coefficients) and apparent optical properties (downwelling attenuation coefficient (K_d) and solar zenith angle (θ, varying 0–60°)). It is found that algorithmic differences in optical parameterizations have a bigger impact on the simulated temperatures in the upper-100 m of the eastern equatorial Pacific, NINO3.4 region, than other parts of the ocean. Overall, the K_dPAR-based approach estimated relatively low surface temperatures compared to those estimated from the chlorophyll-based method. In specific, this cold bias, pronounced in the upper 20–30 m, is speculated to be due to optical characteristics of the algorithm and K_dPAR products, or due to nonlinear hydrodynamical processes involving displacement of mixed-layer depth. Comparisons between each experiment against Global Ocean Data Assimilation System (GODAS; Behringer and Xue 2004) analyses find that KparCLM-based simulations have lower mean differences and variabilities with higher cross-correlation coefficients compared to ChlaCLM- and ChlaID-based experiments.