The acceleration loads automatically calculated by the program are intended to apply ground acceleration. For example, translational acceleration loads are calculated as the negative translational joint mass at a joint times the input acceleration. CSI Analysis Reference Manual, chapter Load Patterns, section Acceleration Loads, has additional information on this.

To apply the acceleration load at the water level, you would need to convert the acceleration time history record to a displacement time history record. Once you have the displacement record, define a Load pattern in which you apply a unit value of joint displacements in the direction of acceleration at the affected joint. For this to affect the structure, you also need to restrain these joints in the direction of loading only. Then create a time history function that will describe a variation of these displacements in time. Finally, define a time history load case that will be specified using both the displacement and the time function.

FAQ

Converting acceleration time history records to displacement time history records

Would it be appropriate for this user to use equations J.2 (provided in Appendix J of the book Static & Dynamic Analysis of Structures by Prof. Wilson) to convert acceleration time history records to displacement time history records?

Yes, that equation can be used to generate displacement history from the ground acceleration history. However, it should be borne in mind that the double integration of ground acceleration records should produce zero displacements at the end of the record. If this does not happen then it may be necessary to apply a base line correction to the displacement record.

Is the base line correction the same procedure as the "Algorithm to Set Displacements at End of Records to Zero" summarized in Table J.1 of Prof. Wilson's book?

Yes, that is one of the various methods available for base line correction.