Natural flows are a complex amalgam of velocity, pressure, and vorticity which often cannot be directly measured or simulated due to their physical interdependence and scaling. Ecohydraulic investigations require not only an accurate description of the natural flow, but must also consider the fluid-body interactions between the indicator organism and the surrounding flow field. In this work, we show how a fish-shaped lateral line probe (LLP) can be used for in-situ flow sensing, including fluid-body interactions in different vertical slot fish passes. The LLP consists of a synchronous collocated sensor array with 16 pressure sensors and two triaxial linear accelerometers with an acquisition frequency of 250 Hz. Using a signal processing workflow with time-domain features based on the Bernoulli equation, the multi-sensor fusion capabilities of the device provide current velocity estimates similar to conventional measuring devices such as acoustic Doppler velocimeters (ADVs). We furthermore show that at velocities > 45 cm/s through the use of a canonical transformation the LLP is capable of producing accurate current velocity estimates even at extreme angular deviations (up to 90°). Finally, it is shown that in contrast to ADV point measurements, the LLP data can be used for spatial flow signature clustering and classification using semantic maps in conjunction with both unsupervised and supervised learning algorithms. Our objective is to showcase the LLP as a new type of ecohydraulic flow measurement and classification device which can be used to simplify the evaluation of natural flows, expanding the analytical capabilities of ecohydraulic investigations.