There are many publications dealing with this issue, and magizines such as Stormwater have resent ideas from various stormwater companies. Urban areas are especially difficult due to extent of infrastructure and impervious areas. Due to lability, best to work with a licensed civil engineer, and consult with hydrologist as needed. As urban areas continue to expand, change, designers should consider this, and consider overdesigning structures. Often costs enter into decisions, and there is always a degree of uncertainty in flood peak estimates. Excessive debris and sediment can cause structure clogging or reduction in capacity. There are ways to address, but building to prevent any possibily of flooding may be impractical or perhaps not possible. Spending resources on signage and education of flowing water hazards may help.
This depends on both the topography and the intensity of rainfall, so no standard rules can be prescribed. However, while surveying for roads, the discharges in the streams are assessed and accordingly drainage structures are designed. Where heavy erosion is expected, protection works as appropriate are also taken-up.