In the proximity of stagnation points, flow instabilities tend to arise at relatively low Reynolds numbers (Re). These instabilities often manifest as vortices that can evolve time-periodic patterns as Re is increased. These types of flows are well studied in cases for which the stagnation point is fixed on an obstacle and the resulting vortices are in the spanwise direction (e.g., the von Kármán vortex street). However, they are less understood in intersecting flows, where the stagnation point is not wall-attached and the resulting vortices are stretched by the flow in the streamwise direction. In this study, quantitative flow velocimetry measurements and three-dimensional numerical simulations are used to characterize two types of steady vortical flow fields in rectangular, intersecting microfluidic geometries with different aspect ratios, α, of the intersecting channels. We show that by changing α, it is possible to precisely tune the features of the steady-state vortical flow field, including the number of vortices, their relative rotation direction, nearby circulation areas, and even vortex core structure. The unique steady-state features determine the onset parameters, dynamics, and frequency of time-periodic fluctuations that develop at higher Re. Our results can be directly applied for enhancing the control over the vortical motion of transported fluids in inertial microfluidics and lab-on-a-chip devices. Additionally, these findings contribute to the fundamental knowledge on vortical motion with the potential to improve the control over vortex-induced vibrations on obstacles in both terrestrial and marine environments.