The county is faced with a number of environmental challenges ranging from air pollution from the quarries and cement factories, water pollution, soil degradation, deforestation, poor solid waste management in the major urban Centres. Less than 10 percent of the households disposed their garbage or solid waste through an organized system

Climate change in the County has seen an increase in intensity and frequency in occurrence of extreme weather events such as severe droughts and floods in Ganze, Kaloleni and Magarini constituencies. These extreme events have had negative socio-economic impacts on almost all sectors such as health, agriculture, environment and tourism. The county is endowed with a wide range of minerals such as Manganese in Ganze constituency, salt in Magarini constituency, coral rocks (stones) in Kilifi South and Kilifi North constituencies, sand in the Entire County, and limestone in Kilifi South constituency and silica in Malindi constituency. Most of these minerals still remain unexploited due to inadequate knowledge on their status, economic viability and appropriate mining technologies.