The Bot River estuary is considered one of the top 10 most important estuaries in the country in terms of its botanical, fish and bird biodiversity. The most contentious issue affecting its management is the frequency of artificial breaching of the mouth. In the past, scientists presumed that the estuary was naturally transforming into a freshwater lake. However, a thorough review established that water abstraction and alien infestation in the catchment had reduced the runoff into the Bot estuary, while artificial breaching of the Kleinmond estuary - to which the Bot is joined via the natural overflow channel at Rooisands into the Lamloch swamps - lowered the water level of the Bot and thus inhibited its natural breaching. Stabilization of the surrounding dunes with alien vegetation had also affected sand transport, which in turn altered the height of the sand berms separating the estuaries from the sea.
The mouth management plan, developed from artificial breaching criteria agreed to at a workshop of specialists and stakeholders in April 2009, stipulate that the Bot water level should reach at least 2.5 metres above mean sea level for the first two years after a breach, unless the salinity drops to 6 parts per thousand (seawater is 35 ppt), which could result in fish mortalities. Artificial breaching of the Kleinmond mouth is not supported. Implementation of the mouth management plan has been approved by the provincial Department of Environmental Affairs & Development Planning (DEADP).
Water quality in the Bot is considered relatively good in terms of faecal pollution, but some nutrient enrichment is likely. The Kleinmond lagoon tends to be contaminated by polluted stormwater, and safe recreational use cannot be guaranteed.
The illegal and unsustainable gillnet fishery that operates in the estuary is a significant threat to the estuary’s value as a nursery area.