Scour depth prediction is a vital issue in bridge pier design. Recently, good progress has been made in the development of artificial intelligence (AI) to predict scour depth around hydraulic structures base such as bridge piers. In this study, two hybrid intelligence models based on combination of group method of data handling (GMDH) with harmony search algorithm (HS) and shuffled complex evolution (SCE) have been developed to predict local scour depth around complex bridge piers using 82 laboratory data measured by authors and 615 data points from published literature. The results were compared to conventional GMDH models with two kinds of transfer functions called GMDH1 and GMDH2. Based upon the pile cap location, data points were divided into three categories. The performance of all utilized models was evaluated by the statistical criteria of R, RMSE, MAPE, BIAS, and SI. Performances of developed models were evaluated by experimental data points collected in laboratory experiments, together with commonly empirical equations. The results showed that GMDH2SCE was the superior model in terms of all statistical criteria in training when the pile cap was above the initial bed level and completely buried pile cap. For a partially-buried pile cap, GMDH1SCE offered the best performance. Among empirical equations, HEC-18 produced relatively good performances for different types of complex piers. This study recommends hybrid GMDH models, as powerful tools in complex bridge pier scour depth prediction.