Measuring rain rates over complex terrain is afflicted with large uncertainties because rain gauges are influenced by orography and weather radars are mostly not able to look into mountain valleys. We apply a new method to estimate near surface rain rates exploiting attenuation data from commercial microwave links in the alpine region of Southern Germany. Received signal level (RSL) data is recorded minutely with small data loggers at the towers and then sent to a database server via GSM. Due to the large RSL fluctuations in periods without rain, the determination of attenuation caused by precipitation is not straightforward. To be able to continuously process the RSL data from July 2010 to October 2010, we introduce a new method to detect wet and dry periods using spectral time series analysis. We show the performance and limitations of the method and analyse the derived rain rates compared to rain gauge and weather radar measurements. The resulting correlations differ for different links and reach values of R2 = 0.80 for the link-gauge comparison and R2 = 0.84 for the link-radar comparison.