Reefs in the Northern Straits of Malacca are exposed to low-light conditions mainly due to sedimentation. Corals can be found in the urban reefs of Pulau Kendi (PK) and Pulau Songsong (PS). Rapid Light Curves (RLCs) measurements were performed in situ using a Diving Pulse Amplitude Modulated (PAM) fluorometer to investigate the photoacclimation of hard corals in the turbid waters of non-protected reefs in PK and PS. Despite the high turbidity at both sites, high derived maximum photochemical efficiency values (Fq′/Fm′(max)) were observed in all coral species at PK (0.77 to 0.80) and PS (0.70 to 0.76). Corals in PS had lower photosynthetic efficiency (α) ranged from 0.08 to 0.09 and maximum relative electron transport rate (rETRmax) ranged from 62.88 ± 6.16 to 136.11 ± 5.70 compared to those in PK (α range: 0.26–0.32; rETRmax range: 102.93 ± 138.41–138.4 ± 5.1). These differences were associated with low non-photochemical quenching (NPQ) (0.08 ± 0.00–0.23 ± 0.00) and symbiont density (0.05 ± 0.00 cells cm2 x 106 – 0.23 ± 0.06 cells cm2 x 106) in PS. The results indicate that coral physiology varies significantly among sites and species, and corals can acclimate to changes in the environment. However, the extent of acclimation depends on light availability in their habitat, which may play a critical role in their survival and persistence in harsh environments.