Start up funding for the UK NMBAQC Scheme was provided by the UK government (Dept. of Environment, Food and Rural Affairs, DEFRA) but the scheme was required to be self funded thereafter. The BEQUALM project (1998-2002) was funded by the European Union but when the NMBAQC scheme was adopted by BEQUALM in 2003, the arrangement for self funding remained. Self funding means the costs for each component or modules within a component needs to be covered by the fees paid by participants. However some additional work areas have been funded, through the scheme, entirely by UK government agencies.

The fees are re-assessed each year by the NMBAQC committee, particularly with the changing contribution of the government agency laboratories (currently funding around 60% of the costs). For each component, fees are estimated on the previous year's level of participation and the projected costs for the year provided by the scheme contractor(s). At present provision of the invertebrate, particle size analysis, and fish modules is contracted APEM, UK, following a competitive tendering process at a European level in 2006. The trial epibiota component (2007-2009) was contracted to Envision, following a competitive tendering process in 2007 and is now provided by the Joint Nature Conservation Committee. The phytoplankton component is currently administered by the Observatorio Canario de Algas Nocivas (OCHABs), and the macroalgae component (2010) is contracted to APEM. The Technical Secretary to NMBAQC is jointly funded by the Environment Agency and the Joint Nature Conservation Committee.

The scheme is not a profit making operation. Any surplus funds generated by specific components are re-invested in subsidisation of workshops, or related projects such as the production of new taxonomic keys, literature lists, or procedural reviews for the benefit of scheme members.