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This presentation addresses some of the methodological challenges associated with the measurement of turbulence and use of scintillometers in the urban RSL. Two small aperture scintillometers were located near the roof top interface in a densely urbanized part of Basel, Switzerland, as part of the Basel Urban Boundary Layer Experiment (BUBBLE) in the summer of 2002. Eddy covariance instruments co-located near the mid-point of each scintillometer path were used to calculate the non-dimensional forms of dissipation rate and structure parameter of temperature used by the scintillometer to calculate the fluxes of momentum and sensible heat. The data show large scatter with little dependence on wind direction (e.g. along-canyon vs. cross-canyon flow) and derivation of fitting functions is difficult. Still, the results suggest that the urban forms of these non-dimensional quantities improve the performance of the scintillometer compared to using conventional Monin-Obukov (MO) equations derived over rural areas. The results also indicate a strong sensitivity of the scintillometer data to the effective measurement height zd above the urban surface which may be more important compared to the influence of using modified MO equations.