A highly accurate and fully implicit algorithm for analyses of transient effects in heated grooved channels, including chaotic responses and transition to secondary states, has been developed. The algorithm can handle pattern interaction problems arising from combinations of geometric and heating patterns which are expected to be beneficial in the development of energy efficient stirring systems. The algorithm uses spectral spatial discretization and up to sixth‐order temporal discretization, providing the means to deliver machine accuracy. The spatial discretization relies on a combination of Chebyshev and Fourier expansions, guaranteeing very good resolution in the vicinity of the grooved walls. The enforcement of boundary conditions along the irregular boundaries is carried out using the immersed boundary conditions. The overall discretization leads to a gridless algorithm and provides the geometric flexibility required for efficient analyses of multitude of topography patterns. Extensive testing demonstrates that the algorithm achieves the theoretically predicted accuracy.