There are increasing threats from environmental degradation to wetland habitats all over the world and the internationally important wetland ecosystem of the Mai Po Marshes Nature Reserve in the north-west quadrant of Hong Kong (P.R. China) is no exception. Polluted tidal water is channelled from the Deep Bay to the traditional shallow shrimp ponds (gei wais), giving rise to growing concerns of potential pollution impacts on the biodiversity and productivity of the valuable wetlands. The present study assessed the pollution status by nutrient contents and faecal bacterial counts of the waterways which drain the gei wais and evaluated the spatial and temporal variations. Biochemical oxygen demand, total nitrogen, ammoniacal nitrogen, total phosphorus, orthophosphate phosphorus and faecal bacteria counts were generally lower in the channel waters from the middle part of the Marshes than those of the southern and/or northern ends, indicating a distinctive spatial pollution pattern across the Marshes.