Escherichia coli are rod-shaped gram-negative bacteria naturally present in the lower intestinal tracts of warm-blooded organisms including humans and are often released into the environment through faecal material and wastewater effluent. The presence of E. coli in waters has long been regarded as an indicator for recent faecal contamination, and possible presence of other more harmful enteropathogens. This study examined the total coliform load and occurrence of E. coli to determine the microbial water quality of Merchang Lagoon on Terengganu coast facing the South China Sea, and Raban Lake, part of the Chenderoh Hydroelectric Dam reservoir in the Lenggong Valley, Perak. Water samples were collected from three sites in the lagoon, and two sites in the lake. Total coliform load in water was enumerated by most probable number (MPN) method, and E. coli isolation was carried out using eosin methylene blue (EMB) agar. The results showed greatly varied total coliform counts from site to site in both the lagoon (site 1: 7; site 2: 220; site 3: 920 CFU/100 mL) and lake (site 1: 220; site 2: 1600 CFU/100 mL). All sites showed presence of E. coli. The results suggest faecal pollution, and the impact of water stagnation and human activities on the coliform load. The impacts of faecal pollution on public health and aquaculture in the investigated areas are discussed. Long-term monitoring of faecal pollution constitutes the essential part of environmental conservation and preservation against the risk of waterborne faecal pathogens in recreational and commercial activities.