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Climate change may alter physical and chemical processes increasing pollution of transitional and coastal waters. Drought conditions, particularly in the south-east of the UK will reduce surface runoff but also dilution of continuous discharges. Drier summers, but more extreme rainfall events, will exacerbate microbial delivery from livestock farming and combined sewage overflows (CSOs) producing intermittent and short term non-compliance in bathing and shellfish harvesting waters. Increased temperature and, in the longer term, decreased pH will affect water and sediment contaminant bioaccumulation and toxicity to marine organisms, in some cases increased degradation and metabolism may reduce toxicity but in other cases increased stress may increase vulnerability.

It is uncertain if water quality change will affect resilient estuarine species or change ecosystem function. Climate change presents challenges to Competent Monitoring Authorities (CMAs) as chemical and microbial pollution of coastal waters has the potential to impact on ecological quality, health, economic resource utilisation and compliance with EU Directives.