Moisture content of biodiesel can be estimated by using conventional Dean and stark method by distilling out the water in the presence of carrier liquid, as it is done for diesel. The end point of transesterification reaction is depends on the raw material and catalyst used in the process. Generally, by using base catalyst 1 hour is enough for the completion of the reaction for oils with lower FFA less than 1-2%. Or else it can be best studied from the literature or from the kinetic study experiments like testing of the samples at regular interval of time and check for the time to reach the equilibrium concentration. the point at which further conversion is stopped can be said as end point, there is no any technique which can estimate the end point physically.
The international standard of water content determination is Karl Fisher method described in EN ISO 12937. The procedure is quick, easy and precise.
The end of transesterification process You can establish by TLC (thin layer chromatography) method . By taking samples during reaction in certain time intervals (eg. 10 mins) , and then compare them during TLC. Disadvantage of this method is that You will know when the process has ended. It can be helpful for the next process.