Ecological services offered by wetlands are intangible in nature and quantification has been a tedious job. Though efforts of the researchers continue, there is still no perfect methodology which has been devised and can be employed straightway.
One way is to find out the depth of water table at regular distances from the wet land & the quality of water from each of them,taking into consideration the chemical nature of underground soil.Another point is to measure the variety of biodiversity in the ecosystem & which of them helps in making the water clear.Monitoring the micro & macro elements & compounds periodically can also say something about nutrient transfer.Nutrient holding capacity of benthic soil can also be checked which will reflect to what extent it differs with nearby terrestrial soil & whether the same needs to be used in nearby agricultural fields, leading to less or nil use of outside fertilizers - though it may not be on a regular basis.
I think, first, we should know exactly the social-ecological system (SES) of the ecosystem. Second, we assess the ecosystem-human need linkage to find how high their value their connectivity to the ecosystem. Third, we measure all ecosystem service related with the local knowledge. And four, we use total economic valuation (TEV) to value ecosystem services. Using TEV, mean we define and measure direct use (UV) and indirect use value (IUV) of the ecosystem, option value (OV), bequest value (BV) and existence value (EV) of the ecosystem.
We can also social-economic-ecological modeling to see the dynamic system of ecosystem-human need linkages, both in economic, social and ecological terms.
We assessed ecosystem services in a tropical coastal wetland in Colombia, using (1) social-ecological history and (2) interviews. The paper is Vilardy et al. (2011) in Hydrological Sciences Journal. I think it is uploaded in my profile, otherwise request to me and I will send you.
ecological values of wetlands may include 1. the value as aquifers, to maintain the water table of the area. 2. water sink & storage for irrigation water as well as survival of the aquatic community, 3. wetland as a component of water cycle