Numerical simulations are conducted to evaluate connectivity and estimate fracture transmissivity, based on field measured borehole flows in sparsely fractured crystalline rock. The data set considered consists of directional fracture-specific flows obtained without pumping, corresponding to natural flow conditions where topography is the main driving force for flow. A method for conditioning transmissivity against the flow measurements is developed and applied for a semi-generic discrete fracture network representation of the bedrock. The model is conditioned against depth-aggregated flows and is able to provide a description of the general features of the subsurface flow system. Results indicate that direct flow-conditioned fracture transmissivities for natural flow conditions can be up to an order of magnitude smaller than transmissivities obtained from flow measurements under pumped conditions and inferred using simplifying homogenisation assumptions. The flow-conditioned transmissivities are shown to be more representative for the regions of bedrock local to the borehole vicinity and consistent with transmissivities obtained from traditional transient pressure response tests. The effect of open boreholes is notable in the field data and its applicability in estimation of upper bounds of the effective vertical transmissivity of rock is significant.