The correct option is
D beside
Option A - 'In' is used to explain 'inside'. As 'holy places' can't be inside the sea, we can't use 'in' here. Thus option A is incorrect.
Option B - 'At' is used to explain 'a particular location'. The sentence explains that the holy places are located next to the sea and not at the sea. As 'sea' is not the exact location where 'holy places' are located, we can't use 'at' here. Thus option B is incorrect.
Option C - 'On' is used to explain 'something/someone that is above'. 'Holy places' can't be placed above 'the sea', hence we can't use 'on' here. Thus option C is incorrect.
Option D - 'Beside' is used to explain 'next to'. As the sentence explains that the 'holy places' are located next to the sea, we can use 'beside' here. Thus option D is the correct answer.
'Most of our holy places, whether on the hills or in the plains, are generally situated along the river-banks or beside the sea.'