Abstract Bayesian belief network ( Fully Connected Belief Networks, FC BeNe) was used to estimate uncertainty in the functioning of established buffer zones in Finland. Four experts in the field of water protection and four in biodiversity were asked to assess the roles of 25 key variables involved in the functioning of buffer zones. The matrix comprised five levels of information: field properties, buffer zone properties, management measures, site data and concerns. The eight experts were asked to estimate probability distributions and causal relationships between the 25 variables, which included in particular erosion, particle bound P, dissolved P, and plant, insect and bird species diversity. Any of the three phases of the analysis; prior distributions, links and posterior distributions are end products which are usable as such. The highest uncertainties were attributed to management measures, e.g. sowing leys, meadow plants, trees and/or bushes and soil removal from the upper end of the field in order to create nutrient-poor meadows. Uncertainties were also seen in P-status, fertilizer and manure changes, transport of dissolved phosphorus, particle bound phosphorus, bird species diversity and landscape. All experts thought that erosion affects particle bound phosphorus, but there was wide deviation in the link strength values, 0.05–0.7, which clearly reflects a lack of knowledge. Two of the experts assumed particle bound P to become partly dissolved, the other two did not. The effect of buffer zones on transport of dissolved phosphorus was not clear. The link strength direction of the variables grazing and rotational grazing to dissolved P varied between the experts. According to the expert evaluations, positive impacts caused by buffer zones were probable in erosion, and in plant and insect species diversity, which is in agreement with existing empirical studies. Experts expected plant height to be beneficial to bird species diversity, but disagreed as to the effect of plant height on plant and insect species diversity. Biodiversity experts considered that steep slopes produced more erosion, more leaching, and hence more patches for biodiversity contrary to water pollution.